Aside from pointing you in the direction of the informational threads from about a year ago, we can't exactly point to a negative, can we?
Edit: To be clear, what I mean to say is it's difficult to prove a negative. It's easier to point to people being banned than people not being banned. I wasn't banned and didn't use illegitimate apps, for example, but that doesn't demonstrate much without also pointing to every single person who wasn't banned and didn't use illegitimate apps. Instead, it's easier to point to the people who came forward about being banned and all of the illegitimate apps they were using. There isn't a confirmed case of anyone being banned for only using CFW, so it's likely that Nintendo banned people for using illegitimate apps. In addition, we understand that one was far less likely to be banned with SpotPass information sharing and Friends List information sharing turned off in the 3DS system settings. This also supports the idea that Nintendo was collecting information on application usage as a method for detecting CFW usage, so it doesn't appear likely that they could directly detect CFW. If you also look at the 3DS operating system and also how CFW works, there doesn't appear to be a mechanism in place that would allow it to detect CFW alone. There's nothing about the operating system that checks for the Luma3DS payload on the SD card or signature patches, for example. What we do see is a mechanism in place to detect which applications are being run and an ability to send that information to Nintendo.